Nesvilab FragPipe issues

Nesvilab / FragPipe

A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data

http://fragpipe.nesvilab.org

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issues

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Skyline Error: The document does not contain any peptides.

#1654 azying312 opened 12 hours ago
3
possible fix for #1652

#1653 guoci opened 13 hours ago
3
Browse directly to pasted folder in "Choose raw data files dialog"

#1652 chambm opened 17 hours ago
8
How to add diagnostic ion and how to check the results

#1651 douyue623 opened 20 hours ago
2
problem with configuration

#1650 Ale-ksa-ndra closed 2 days ago
5
LFQ-phospho - sequence

#1649 nishimuy opened 3 days ago
2
Error happened when analyzing ddaPASEF (glycopeptide) with FragPipe (V22).

#1648 andyzim111 closed 2 days ago
2
SpecLib Generation Issue

#1647 azying312 opened 3 days ago
17
Change UI Scaling

#1646 tjlundgren closed 3 days ago
2
Process 'MSBooster' finished, exit code: 1, java.lang.NullPointerException

#1645 ciancone94 closed 4 days ago
2
Questions about diaTracer and endogenous peptides search

#1644 ako81818 closed 20 hours ago
11
How to match Chromatogram peak with Protein ID?

#1643 BjoernZiehr closed 20 hours ago
7
Instrument not detected, how to specify?

#1642 BjoernZiehr closed 6 days ago
5
Summary table-like output for FragPipe

#1641 carlosg-czbiohub opened 1 week ago
1
Incorrect settings broke PTMProphet

#1639 brunoalex7 closed 1 week ago
8
FP 22.0, plexDIA & MSBooster

#1638 kabalak opened 1 week ago
4
MS1 quantitation IonQuant error

#1637 Angelwitch closed 1 week ago
4
SpecLibGen fails in FragPipe 22.0; "A module that was compiled using NumPy 1.x cannot be run in NumPy 2.0.0"

#1636 jossmi closed 1 week ago
7
A user thought there was a small bug in the latest version of fragpipe, but actually there wasn't

#1635 crf2213 closed 1 week ago
1
SaintExpress Analysis after GPF-DIA?

#1634 TTCooper-PhD opened 1 week ago
1
Incompatible options: MSFragger-DIA split database is incompatible with DIA, GPF-DIA, DIA-Lib, or DDA+ data types

#1633 helloworld1631 closed 2 weeks ago
3
Downstream SAINTexpress non-zero exit code

#1632 FlyOB closed 2 weeks ago
4
java.lang.ArrayIndexOutOfBoundsException: Index 1200 out of bounds for length 1200

#1631 trungttt closed 2 weeks ago
1
FragPipe v22 + DIA-NN 1.9 - Failed to generate skyline document

#1630 emhumphries opened 2 weeks ago
3
Failure to propagate to DIA-NN output

#1629 BrendonSeale closed 2 weeks ago
3
Site specific variable mod search

#1628 Jack-Moen closed 2 weeks ago
5
Python package version incompatibility: ValueError: Multi-dimensional indexing (e.g. obj[:, None]) is no longer supported. Convert to a numpy array before indexing instead.

#1627 actopossum closed 2 weeks ago
4
FragPipe could not download MSFragger with message error like the image. I manually download MSFragger and put it under Tools folder of FragPipe, but when I browse the folder by FragPipe, I could not see .jar document in MSFragger folder.

#1626 Pom22 closed 2 weeks ago
4
FragPipe 22.0 requires EasyPQP 0.1.44+

#1625 jasminesmn closed 2 weeks ago
2
Group FDR

#1624 BenSamy2020 closed 2 weeks ago
1
java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: Index 1200 out of bounds for length 1200

#1623 naiyoubuding opened 2 weeks ago
7
Percolator: Exception caught: ERROR: Could not open the file for writing. Check if the folder exists and if you have permission to write.

#1622 trungttt closed 2 weeks ago
4
How to process RAW files from Astral using FragPipe?

#1621 andyzim111 closed 2 weeks ago
1
Python Version

#1620 Meera-Asokan closed 2 weeks ago
7
Combining results from different workflows

#1619 cybastam closed 2 weeks ago
1
Question about multiple space search (e.g. canonical and non-canonical)

#1618 hupak2022 closed 2 weeks ago
1
No identifications for ETCID?

#1617 rolivella closed 3 weeks ago
4
MSBooster shows an error for non-specific HLA peptidomics - timsTOF data

#1616 mshahbazy closed 2 weeks ago
7
MSFragger Error: java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError: Java heap space

#1615 rabdo17 closed 2 weeks ago
2
Process 'MSBooster' finished, exit code: 1 Process returned non-zero exit code, stopping

#1614 PietroCrivello closed 3 weeks ago
3
Warning: not enough target PSMs are available for regression.

#1613 amingson closed 3 weeks ago
4
Fragpipe 22 doesn't generate MSStats csv output file

#1612 bnewt2k closed 3 weeks ago
8
The 2-D scan index in SCIEX data broke MSFragger and other tools.

#1611 solabthomas closed 2 weeks ago
4
Peaks with unreasonable large mz broke MSFragger

#1610 amingson opened 3 weeks ago
4
Can the fragpipe analyze the dimethylation-peptides?

#1609 ningzaizia closed 2 weeks ago
40
Process 'WriteSubMzml' finished, exit code: 1

#1608 lbwfff closed 2 weeks ago
6
failed to generate skyline document with v22.0 because the users didn't run any other modules

#1607 wtbxsjy closed 2 weeks ago
2
Fragpipe v22.0 error with DIA-PASEF file

#1606 hcadre opened 3 weeks ago
13
Linux: Fragpipe Headless Thermo Native Libraries Not Detected

#1605 Sanpme66 closed 3 weeks ago
2
Failed in reading frame (intensity is larger than the maximum allowed value)

#1604 tomi3636 opened 3 weeks ago
2